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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtactctgaaaatcattgtgttcaaaatgtaattgaacatacatgtggtcttatcaagaataagtacaataatatattgattggaaatattggaa...

Basic information

species Zea mays
transcript GRMZM2G017089_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017089_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os03g21990.1 (Oryza sativa), 5'ss of exon 16
GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtactctgaaaatcattgtgttcaaa--------------atgtaattgaacatacatgtggtcttat-caagaataagtacaataatatattgattggaaatattggaa--------------------------------------------------------------
||| ||||||||||| || || || ||||||||||||||||| ||||||||||||||||||||||||| || | | |  ||| ||| | |||                  || | ||| || | | |  |||| | ||  |   |  | | |  || | | |    |  |  |  |||                                                                
GTCCCAGCAGAAAACCATCATAAACTCAATGGCTGTAAATGAAGATGGTGTCTTGGCAACTGGAGgta-tgcattgttgaaaacatcgagtttttgcctccttcctatttattttattaaagaaaaagatggtttaatgtatttagtaatgctgtattttctatgctatacttgctggccgcaaccgattcaataaaattttttgcagatcatattattaaaagtagtaatatcttgtgcag

upper sequence: GRMZM2G017089_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT4G15900.1 (Arabidopsis thaliana), 5'ss of exon 15
GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgta-atgtac-tctgaaaatcattgtgttcaaaatgtaattgaacatacatgtggtcttatcaagaataag-tacaataatatattgattggaaatattggaa-----------------
 ||||| |||||||| ||||| ||| ||||||||||||| |||||||||||  |||  |||||||||| ||   | | |   | || ||  || |    ||| ||||    | | | || |  ||  | |  | ||  | ||| || | |  | || || |  |   |                 
TTCGCAACAGAAAACCATAATTAATGCAATGGCTGTAAACGAGGATGGTGTGATGGTCACTGGAGgtatataatcatttctgattcctttcgtccc---tgtgattg--ttttcctttgatagtaaaatgggtgagacataatcat-tttcaactgaaactgattctatatatgtgtgaatgaag
















Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|78021762|gb|DV490149.1|DV490149
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|148951459|gb|EC897184.2|EC897184
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|60342895|gb|DN209868.1|DN209868
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|37376961|gb|CF625047.1|CF625047
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|116814103|gb|EC856623.1|EC856623
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTA
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|71432304|gb|DR813354.1|DR813354
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|31406178|gb|CD484910.1|CD484910
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|32933315|gb|CF038127.1|CF038127
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTTTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|60357310|gb|DN224283.1|DN224283
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|93012802|gb|EB638322.1|EB638322
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|110491423|gb|EE013510.1|EE013510
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|78023548|gb|DV491935.1|DV491935
EST:     GCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: GCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|6538870|gb|AW225009.1|AW225009
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTTTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|71757914|gb|DR955851.1|DR955851
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|33093989|gb|CF053983.1|CF053983
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTTTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|4967045|gb|AI691809.1|AI691809
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|33091991|gb|CF051985.1|CF051985
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTTTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|6865096|gb|AW360446.1|AW360446
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTTTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|5055899|gb|AI734786.1|AI734786
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|101383542|gb|EB813827.1|EB813827
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|148950912|gb|EC896542.2|EC896542
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|37382890|gb|CF628417.1|CF628417
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|148943610|gb|EC888673.2|EC888673
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|71432303|gb|DR813353.1|DR813353
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|33091976|gb|CF051970.1|CF051970
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTTTTGGCAACTGGAG                         GGGATAATGGAAGCCTGCGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|33091634|gb|CF051628.1|CF051628
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTTTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
EST: gi|31909551|gb|CD650975.1|CD650975
EST:     AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAG                         GGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC
genomic: AATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 256

GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 97

GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 180

GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtact ... acctgtgcagGGGATAATGGAAGCCTGTGGTTTTGGGACTGGAAGAGTGGTCATAACTTTCAACAAGATCAGACTATAGTCCAGCCTG


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCGCAGCAGAAAACAATAATCAATTCAATGGCTGTAAATGAGGATGGTGTCTTGGCAACTGGAGgtaatgtactctgaaaatcattgtgttcaaaatgtaattgaacatacatgtggtcttatcaagaataagtacaataatatattgattggaaatattggaa

- - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaatca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aagaataa